The problem of analysing single-cell data from multiple tissues of the same individual

[zhoudreames]

Hi，I am honored to be able to use the Scomatic software you have developed. I have a problem, I have a question that I hope you can help me. Thanks~
In my study, I sequenced single-cell data from 50 different tissues from the same individual. Would it be better for me to choose to analyse each tissue bam file individually, or would it be better to combine all the different cell type bam files produced by all the tissues？

[zhoudreames]

@isidroc @Francesc-Muyas @helrick I am so sorry to disturb you ，would you help me ？